An LC-MS method based on iTRAQ labeling and high resolution FT-OrbiTrap mass spectrometry was used for the proteomic analysis of 23 human ThinPrep cervical smear specimens. The analysis of three 8-plex sample sets yielded the identification of over 3200 unique proteins at FDR < 1%, of which over 2300 proteins were quantitatively profiled in at least one of the three experiments.

Weak anion exchange ( WAX ) separation of a single SCX fraction, derived from a phosphopeptide enriched sample results in more phosphopeptide Ids than SCX fractionation alone, using the same measurement time.

6.3E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

5.73E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.92E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.62E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.72E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.69E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.29E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.24E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.92E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.68E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.57E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.45E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.71E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.53E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.48E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.46E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.38E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.33E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.31E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.29E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.27E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.25E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.17E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.16E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.14E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.1E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

1.09E1Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

8.88E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

8.64E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

7.82E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

7.16E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

6.47E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

6.21E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

6E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

5.73E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.8E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

4.07E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.7E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.66E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.46E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.22E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

3.01E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.94E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.44E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.35E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.34E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.34E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.33E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.24E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.

2.14E0Parts per MillionThe number of spectral counts (SC) is approximately proportional to the product of the protein concentration and molecular weight (MW), therefore we estimate the fraction of total molecules in parts per million (PPM) by $$PPM_i={SC_i\/MW_i}/∑↙{j=1}↖n {SC_j\/MW_j}$$ where MWi is the molecular weight and SCi is the number of spectral counts for protein i and the summation in the denominator is over all the proteins identified in the experiment for a given tissue and condition.